Could it be that your duct roughness and air density settings are way off in your duct system definition?
In a out of the box template here's what I did:
Copied the Standard duct system, named as Standard 0.07in
On the Design Parameters tab, made sure that Friction was selected, and set to 0.07in
Roughness set to 0.0003 ft
Density set to 0.07508 lbm/ft3
Used the DuctAdd command, set the capacity to 1000 cfm, set duct to round, and clicked the calculate button... got 14.5" size (could restrict to 14" if I removed half inch sizes from catalog). 0.0742", 872.0fpm
Set shape to rectangular, set width to 25", clicked the height calculator, got 8", 0.0656", 720.0 fpm
Set the width to 14", click height calculator got 13" (perhaps 14" if I removed odd sizes from catalog), 0.681", 791.2 fpm
Set the height to 8", click width calculator, got 24" , 0.0715", 750.0fpm
The velocity of a 25x8 duct is going to be 720 fpm, not 1200
25in x 8 in = 200 sq in
1000 cfm / (200 sq in / 144 sq in per ft) = 720
The other velocities reported by AutoCAD MEP check out as well.
Martin Schmid
Product Line Manager
Mechanical Detailing and Electrical Design
Architecture, Engineering, and Construction
Autodesk, Inc.